This question asks whether every family $\mathcal A\subseteq\mathcal P(X)$ is contained in a countably generated
$\sigma$-algebra. (The OP stipulates that $\mathcal A$ is itself a $\sigma$-algebra, but that clearly doesn't matter.) The answers provide counterexamples with either $|\mathcal A|\gt2^{\aleph_0}$ or $|X|=2^{2^{\aleph_0}}.$ I would like to see a counterexample with $|\mathcal A|\le2^{\aleph_0}$ and $|X|\le2^{\aleph_0}.$
Question. Is there a family $\mathcal A\subset\mathcal P(\mathbb R)$ such that $|\mathcal A|\le2^{\aleph_0}$ and $\mathcal A$ is not contained in any countably generated $\sigma$-algebra?